/*
 * This program is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; either version 2 of the License, or
 * (at your option) any later version.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
 */

/*
 * FromFile.java
 * Copyright (C) 2004 University of Waikato, Hamilton, New Zealand
 * 
 */
package weka.classifiers.bayes.net.search.fixed;

import weka.classifiers.bayes.BayesNet;
import weka.classifiers.bayes.net.BIFReader;
import weka.classifiers.bayes.net.ParentSet;
import weka.classifiers.bayes.net.search.SearchAlgorithm;
import weka.core.Instances;
import weka.core.Option;
import weka.core.RevisionUtils;
import weka.core.Utils;

import java.util.Enumeration;
import java.util.Vector;

/**
 * <!-- globalinfo-start --> The FromFile reads the structure of a Bayes net
 * from a file in BIFF format.
 * <p/>
 * <!-- globalinfo-end -->
 * 
 * <!-- options-start --> Valid options are:
 * <p/>
 * 
 * <pre>
 * -B &lt;BIF File&gt;
 *  Name of file containing network structure in BIF format
 * </pre>
 * 
 * <!-- options-end -->
 * 
 * @author Remco Bouckaert
 * @version $Revision: 1.8 $
 */
public class FromFile extends SearchAlgorithm {

	/** for serialization */
	static final long serialVersionUID = 7334358169507619525L;

	/** name of file to read structure from **/
	String m_sBIFFile = "";

	/**
	 * Returns a string describing this object
	 * 
	 * @return a description of the classifier suitable for displaying in the
	 *         explorer/experimenter gui
	 */
	public String globalInfo() {
		return "The FromFile reads the structure of a Bayes net from a file "
				+ "in BIFF format.";
	}

	/**
	 * 
	 * @param bayesNet
	 * @param instances
	 *            the instances to work with
	 * @throws Exception
	 *             if attribute from BIF file could not be found
	 */
	public void buildStructure(BayesNet bayesNet, Instances instances)
			throws Exception {
		// read network structure in BIF format
		BIFReader bifReader = new BIFReader();
		bifReader.processFile(m_sBIFFile);
		// copy parent sets
		for (int iAttribute = 0; iAttribute < instances.numAttributes(); iAttribute++) {
			int iBIFAttribute = bifReader.getNode(bayesNet
					.getNodeName(iAttribute));
			ParentSet bifParentSet = bifReader.getParentSet(iBIFAttribute);
			for (int iBIFParent = 0; iBIFParent < bifParentSet.getNrOfParents(); iBIFParent++) {
				String sParent = bifReader.getNodeName(bifParentSet
						.getParent(iBIFParent));
				int iParent = 0;
				while (iParent < instances.numAttributes()
						&& !bayesNet.getNodeName(iParent).equals(sParent)) {
					iParent++;
				}
				if (iParent >= instances.numAttributes()) {
					throw new Exception("Could not find attribute " + sParent
							+ " from BIF file in data");
				}
				bayesNet.getParentSet(iAttribute).addParent(iParent, instances);
			}
		}
	} // buildStructure

	/**
	 * Set name of network in BIF file to read structure from
	 * 
	 * @param sBIFFile
	 *            the name of the BIF file
	 */
	public void setBIFFile(String sBIFFile) {
		m_sBIFFile = sBIFFile;
	}

	/**
	 * Get name of network in BIF file to read structure from
	 * 
	 * @return BIF file name
	 */
	public String getBIFFile() {
		return m_sBIFFile;
	}

	/**
	 * Returns an enumeration describing the available options.
	 * 
	 * @return an enumeration of all the available options.
	 */
	public Enumeration listOptions() {
		Vector newVector = new Vector();

		newVector.addElement(new Option(
				"\tName of file containing network structure in BIF format\n",
				"B", 1, "-B <BIF File>"));

		Enumeration en = super.listOptions();
		while (en.hasMoreElements())
			newVector.addElement(en.nextElement());

		return newVector.elements();
	}

	/**
	 * Parses a given list of options.
	 * <p/>
	 * 
	 * <!-- options-start --> Valid options are:
	 * <p/>
	 * 
	 * <pre>
	 * -B &lt;BIF File&gt;
	 *  Name of file containing network structure in BIF format
	 * </pre>
	 * 
	 * <!-- options-end -->
	 * 
	 * @param options
	 *            the list of options as an array of strings
	 * @throws Exception
	 *             if an option is not supported
	 */
	public void setOptions(String[] options) throws Exception {
		setBIFFile(Utils.getOption('B', options));

		super.setOptions(options);
	}

	/**
	 * Gets the current settings of the search algorithm.
	 * 
	 * @return an array of strings suitable for passing to setOptions
	 */
	public String[] getOptions() {
		String[] superOptions = super.getOptions();
		String[] options = new String[2 + superOptions.length];
		int current = 0;

		options[current++] = "-B";
		options[current++] = "" + getBIFFile();

		// insert options from parent class
		for (int iOption = 0; iOption < superOptions.length; iOption++) {
			options[current++] = superOptions[iOption];
		}

		// Fill up rest with empty strings, not nulls!
		while (current < options.length) {
			options[current++] = "";
		}
		return options;
	}

	/**
	 * Returns the revision string.
	 * 
	 * @return the revision
	 */
	public String getRevision() {
		return RevisionUtils.extract("$Revision: 1.8 $");
	}

} // class FromFile
